Repositories list

• merfish3d-analysis

  Public
  GPU accelerated post-processing for 2D or 3D iterative barcoded FISH data.

  gpu-accelerationspatial-dataimage-analysis+ 3microscopyspatial-transcriptomicsmerfish

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•6•5•3•Updated Jul 23, 2025Jul 23, 2025

• 2025-CBP-SummerSchool

  Public
  2025 ASU Center for Biological Physics Summer School

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jul 19, 2025Jul 19, 2025

• deeds-registration

  Public
  Python wrapper around DEEDS - efficient algorithm for 3D discrete deformable image registration, reaching the highest accuracy in several benchmarks

  C

  •

  MIT License

  •4•0•0•0•Updated Jul 14, 2025Jul 14, 2025

• dpc-3d

  Public
  Python

  •

  Other

  •0•0•0•1•Updated Jul 14, 2025Jul 14, 2025

• navigate

  Public
  navigate - open source light-sheet microscope controls

  Python

  •

  Other

  •11•0•0•0•Updated Jul 11, 2025Jul 11, 2025

• opm-v2

  Public
  GUI and code for controlling an oblique plane microscope with projection imaging, sensorless adaptive optics, and integrated microfluidics.

  microscopyadaptive-opticsfluidics+ 2lightsheetpymmcore-plus

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•2•1•Updated Jun 24, 2025Jun 24, 2025

• opm-processing-v2

  Public
  Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•4•0•0•Updated Jun 22, 2025Jun 22, 2025

• U-FISH

  Public
  Deep learning based spot detection for FISH images.

  Jupyter Notebook

  •

  MIT License

  •6•1•0•0•Updated Jun 10, 2025Jun 10, 2025

• trackastra

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •21•0•0•1•Updated Apr 25, 2025Apr 25, 2025

• OPM

  Public archive
  Archived: control, reconstruction, and analysis code for oblique plane microscopy.

  experimentphysicsgpu-acceleration+ 4imagingtimelapsemicromanagerlightsheet

  Python

  •

  GNU General Public License v3.0

  •7•22•0•2•Updated Apr 1, 2025Apr 1, 2025

• BaSiCPy

  Public
  Python

  •

  MIT License

  •24•1•0•0•Updated Mar 29, 2025Mar 29, 2025

• pycrofluidics

  Public
  A Python module for controlling Elveflow microfluidic devices

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Dec 14, 2024Dec 14, 2024

• mcSIM

  Public
  Code for running a multicolor structured illumination microscopy (SIM) experiment using a DLP6500 digital micromirror device (DMD) and performing SIM reconstruction.

  experimentphysicssim+ 4imagingdmdmicromanagersimulation

  Python

  •

  GNU General Public License v3.0

  •15•58•0•1•Updated Dec 12, 2024Dec 12, 2024

• napari-micromanager

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •22•0•0•0•Updated Sep 28, 2024Sep 28, 2024

• instanseg

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •31•0•0•0•Updated Sep 10, 2024Sep 10, 2024

• rlgc

  Public
  Richardson-Lucy deconvolution with local stopping given by gradient consensus

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•0•0•0•Updated Sep 1, 2024Sep 1, 2024

• SPIM_model

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Aug 30, 2024Aug 30, 2024

• ray_trace_pb

  Public
  Simple ray tracing in Python

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

• sparse-deconv-py

  Public
  Official Python implementation of the 'Sparse deconvolution'-v0.3.0

  Python

  •

  Open Data Commons Open Database License v1.0

  •18•1•0•0•Updated Jul 16, 2024Jul 16, 2024

• localize-psf

  Public
  Code for localizing diffraction limited fluorescent objects and fitting the results to various different point-spread function (PSF) models.

  python

  Python

  •

  GNU General Public License v3.0

  •2•5•0•0•Updated Jul 3, 2024Jul 3, 2024

• spots3d

  Public
  GPU accelerated spot finding and localization for both skewed (diSPIM, lattice, OPM) and standard geometry (widefield, confocal) 3D microscopy data.

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 30, 2024Mar 30, 2024

• napari-spot-detection

  Public
  Detect diffraction limited spots in 2D and 3D, in standard or skewed microscopy images.

  Python

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Feb 28, 2024Feb 28, 2024

• ProjectionSimulation

  Public
  Simple simulation to compare standard and projection imaging

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 9, 2023Oct 9, 2023

• Gpufit

  Public
  GPU-accelerated Levenberg-Marquardt curve fitting in CUDA

  Cuda

  •

  MIT License

  •95•1•0•0•Updated Aug 11, 2023Aug 11, 2023

• napari-mcsim

  Public
  Napari plugin automating structured illumination microscopy (SIM) reconstruction and diagnostics from the mcSIM package

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Aug 2, 2023Aug 2, 2023

• npy2bdv

  Public
  Fast writing of numpy 3d-arrays into HDF5 and N5 Fiji/BigDataViewer files.

  Python

  •

  GNU General Public License v3.0

  •12•0•0•0•Updated May 17, 2023May 17, 2023

• rDL-SIM

  Public
  A Tensorflow implementation of rationalized deep learning (rDL) based image denoising for microscopy images

  Python

  •

  MIT License

  •6•0•0•0•Updated Oct 12, 2022Oct 12, 2022

• I2K2022-SIM

  Public
  I2K 2022 mcSIM tutorial

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated Jun 8, 2022Jun 8, 2022

• MVRegFus

  Public
  Python module for registering and fusing multi-view microscopy data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•0•0•0•Updated May 16, 2021May 16, 2021

• IDT-using-Annular-Illumination

  Public
  This is the MATLAB Implementation for Annular Illumination Intensity Diffraction Tomography (aIDT).

  MATLAB

  •

  BSD 3-Clause "New" or "Revised" License

  •9•0•0•0•Updated May 12, 2020May 12, 2020